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CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters
DC Field | Value | Language |
---|---|---|
dc.contributor.author | van den Belt, Matthias | - |
dc.contributor.author | Gilchrist, Cameron | - |
dc.contributor.author | Booth, Thomas J. | - |
dc.contributor.author | Chooi, Yit-Heng | - |
dc.contributor.author | Medema, Marnix H. | - |
dc.contributor.author | Alanjary, Mohammad | - |
dc.date.accessioned | 2023-08-17T02:05:26Z | - |
dc.date.available | 2023-08-17T11:05:51Z | - |
dc.date.issued | 2023-05-03 | - |
dc.identifier.citation | BMC Bioinformatics, Vol.24(1):181 | ko_KR |
dc.identifier.issn | 1471-2105 | - |
dc.identifier.uri | https://hdl.handle.net/10371/195387 | - |
dc.description.abstract | Background
Co-localized sets of genes that encode specialized functions are common across microbial genomes and occur in genomes of larger eukaryotes as well. Important examples include Biosynthetic Gene Clusters (BGCs) that produce specialized metabolites with medicinal, agricultural, and industrial value (e.g. antimicrobials). Comparative analysis of BGCs can aid in the discovery of novel metabolites by highlighting distribution and identifying variants in public genomes. Unfortunately, gene-cluster-level homology detection remains inaccessible, time-consuming and difficult to interpret. Results The comparative gene cluster analysis toolbox (CAGECAT) is a rapid and user-friendly platform to mitigate difficulties in comparative analysis of whole gene clusters. The software provides homology searches and downstream analyses without the need for command-line or programming expertise. By leveraging remote BLAST databases, which always provide up-to-date results, CAGECAT can yield relevant matches that aid in the comparison, taxonomic distribution, or evolution of an unknown query. The service is extensible and interoperable and implements the cblaster and clinker pipelines to perform homology search, filtering, gene neighbourhood estimation, and dynamic visualisation of resulting variant BGCs. With the visualisation module, publication-quality figures can be customized directly from a web-browser, which greatly accelerates their interpretation via informative overlays to identify conserved genes in a BGC query. Conclusion Overall, CAGECAT is an extensible software that can be interfaced via a standard web-browser for whole region homology searches and comparison on continually updated genomes from NCBI. The public web server and installable docker image are open source and freely available without registration at: https://cagecat.bioinformatics.nl. | ko_KR |
dc.description.sponsorship | M.A is supported by the NWO Talent programme Veni science domain (VI.Veni.202.130). C.L.M.G is supported by the Australian Government Research Training Project (RTP) Ph.D. scholarship, the National Research Foundation of Korea (NRF) [2021R1C1C1012065, 2019R1A6A1A10073437], the Samsung DS research fund program and the Creative-Pioneering Researchers Program through Seoul National University. Y-H.C is supported by an Australian Research Council Future Fellowship (FT160100233). M.H.M. is supported by an ERC Starting Grant (948770-DECIPHER to M.H.M.). | ko_KR |
dc.language.iso | en | ko_KR |
dc.publisher | BMC | ko_KR |
dc.subject | Gene cluster | - |
dc.subject | Secondary metabolite | - |
dc.subject | Homology search | - |
dc.subject | Colocalized | - |
dc.subject | Biosynthetic | - |
dc.subject | Comparative analysis | - |
dc.title | CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters | ko_KR |
dc.type | Article | ko_KR |
dc.identifier.doi | 10.1186/s12859-023-05311-2 | ko_KR |
dc.citation.journaltitle | BMC Bioinformatics | ko_KR |
dc.language.rfc3066 | en | - |
dc.rights.holder | The Author(s) | - |
dc.date.updated | 2023-05-07T03:11:11Z | - |
dc.citation.number | 181 | ko_KR |
dc.citation.volume | 24 | ko_KR |
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